Source code for utils.extract_atoms
#!/usr/bin/env python3
"""Module containing the ExtractAtoms class and the command line interface."""
import argparse
import re
from pathlib import Path
from typing import Optional
from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_structure_utils.gro_lib.gro import Gro
from biobb_structure_utils.utils.common import PDB_SERIAL_RECORDS
[docs]
class ExtractAtoms(BiobbObject):
"""
| biobb_structure_utils ExtractAtoms
| Class to extract atoms from a 3D structure.
| Extracts all atoms from a 3D structure that match a regular expression pattern.
Args:
input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/2vgb.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
output_structure_path (str): Output structure file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/OE2_atoms.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **regular_expression_pattern** (*str*) - ("^D") Python style regular expression matching the selected atom names.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
Examples:
This is a use example of how to use the building block from Python::
from biobb_structure_utils.utils.extract_atoms import extract_atoms
prop = {
'regular_expression_pattern': '^D'
}
extract_atoms(input_structure_path='/path/to/myStructure.pdb',
output_structure_path='/path/to/newStructure.pdb',
properties=prop)
Info:
* wrapped_software:
* name: In house
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self, input_structure_path, output_structure_path, properties=None, **kwargs
) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {"input_structure_path": input_structure_path},
"out": {"output_structure_path": output_structure_path},
}
# Properties specific for BB
self.regular_expression_pattern = properties.get(
"regular_expression_pattern", "^D"
)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`ExtractAtoms <utils.extract_atoms.ExtractAtoms>` utils.extract_atoms.ExtractAtoms object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Business code
extension = Path(self.io_dict["in"]["input_structure_path"]).suffix.lower()
if extension.lower() == ".gro":
fu.log(
"GRO format detected, extracting all atoms matching %s"
% self.regular_expression_pattern,
self.out_log,
)
gro_st = Gro()
gro_st.read_gro_file(self.io_dict["in"]["input_structure_path"])
gro_st.select_atoms(self.regular_expression_pattern)
if gro_st.num_of_atoms:
fu.log(
"%d atoms found writting GRO file" % gro_st.num_of_atoms,
self.out_log,
self.global_log,
)
gro_st.write_gro_file(self.io_dict["out"]["output_structure_path"])
else:
fu.log(
"No matching atoms found writting empty GRO file",
self.out_log,
self.global_log,
)
open(self.io_dict["out"]["output_structure_path"], "w").close()
else:
fu.log(
"PDB format detected, extracting all atoms matching %s"
% self.regular_expression_pattern,
self.out_log,
)
# Direct aproach solution implemented to avoid the
# issues presented in commit message (c92aab9604a6a31d13f4170ff47b231df0a588ef)
# with the Biopython library
atoms_match_cont = 0
with open(
self.io_dict["in"]["input_structure_path"], "r"
) as input_pdb, open(
self.io_dict["out"]["output_structure_path"], "w"
) as output_pdb:
for line in input_pdb:
record = line[:6].upper().strip()
if (
len(line) > 10 and record in PDB_SERIAL_RECORDS
): # Avoid MODEL, ENDMDL records and empty lines
pdb_atom_name = line[12:16].strip()
if re.search(self.regular_expression_pattern, pdb_atom_name):
atoms_match_cont += 1
output_pdb.write(line)
if atoms_match_cont:
fu.log(
"%d atoms found writting PDB file" % atoms_match_cont,
self.out_log,
self.global_log,
)
else:
fu.log(
"No matching atoms found writting empty PDB file",
self.out_log,
self.global_log,
)
self.return_code = 0
##########
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def extract_atoms(
input_structure_path: str,
output_structure_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Execute the :class:`ExtractAtoms <utils.extract_atoms.ExtractAtoms>` class and
execute the :meth:`launch() <utils.extract_atoms.ExtractAtoms.launch>` method."""
return ExtractAtoms(
input_structure_path=input_structure_path,
output_structure_path=output_structure_path,
properties=properties,
**kwargs,
).launch()
[docs]
def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(
description="Remove the selected ligand atoms from a 3D structure.",
formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
)
parser.add_argument(
"-c",
"--config",
required=False,
help="This file can be a YAML file, JSON file or JSON string",
)
# Specific args of each building block
required_args = parser.add_argument_group("required arguments")
required_args.add_argument(
"-i", "--input_structure_path", required=True, help="Input structure file name"
)
required_args.add_argument(
"-o",
"--output_structure_path",
required=True,
help="Output structure file name",
)
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call of each building block
extract_atoms(
input_structure_path=args.input_structure_path,
output_structure_path=args.output_structure_path,
properties=properties,
)
if __name__ == "__main__":
main()